Figure 3

Data preprocessing

Processing tables

Defining MSI subjects by whether more than 10% of their mutations are deletion over 1bp:

Figure 3A

Cell division timing

Loading in clinical data

Plotting MRCA divisions of cancers and adenomas:

N for each boxplot

Plotting age and divisions to MRCA:

Processing data from intestinal stem cell colonies

Markerlengths for the ISC colonies:

Distance from the root needs to be subtracted manually, as the blood or bulk samples represent the germline genotype:

Getting the minimum number of marker all samples agree on, as long as that's more than 70% of the maximum possible markers

Saving heatmaps with patient ages

Calculating L1 distance and cell divisions

Creating function to go through each sample separately

Manually annotating from supplementary information of Naxerova et al 2017.

Plotting days per division:

How often do samples divide after tumor initation?

Fig. 3E

Showing the time from cancer initation to each sample type:

Kruskal Wallis test across all groups.

Extended Data Figure 6b

Extended Data Figure 6c

Fig 3F

Plotting individual trees

Figure 3H

Metastasis private branches

Sample numbers

Sample numbers

Fig 3I

Comparing metachronous metastases separately

Extended Data Fig 4

Bootstrapping key steps of cancer evolution on the patient level.

Cancer MRCA of all cases

Primary tumor diversification

Primary tumor diversification

Distant metastasis divergence

Lymph node metastasis divergence

Fig 3J

Divisions of primary tumor sample clostest to mets

Same analysis for lymph node metastases:

Timing when metastases could have diverged

Years from cancer MRCA to metastasis divergence

Fig 3K

Estimating effective division rate

Numbers for the text

Number of MMRd and MMRp samples

Sample numbers for first paragraph:

Cell divisions to cancer MRCA

Cell divisions to adenoma MRCA

ISC donor ages

Divisions since tumor MRCA per sample type. Only synchronous distant metastases.

Divergence and diversification timing from cancer MRCA

Patients with metastasis divergence before primary tumor diversification.

Division times of metastases seeding primary tumor regions:

Numbers for last paragraph of section for Fig 3

Total number of cell divisions across all samples.

Number of PT regions per subject

Sample number in Hu et al

Mutation burden in polyGs in Hu/Curtis data

C66 division burden